Juergen Rose
2014-May-18 05:16 UTC
[R] dev-lang/R-3.1.0: biocLite("vsn") removes all files in /
I had the following files in /: root at caiman:/root(8)# ll / total 160301 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log lrwxrwxrwx 1 root root 11 Jan 22 2011 data -> data_caiman/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ lrwxrwxrwx 1 root root 23 Dec 29 13:43 data_impala -> /net/impala/data_impala/ lrwxrwxrwx 1 root root 21 Jan 27 08:13 data_lynx2 -> /net/lynx2/data_lynx2/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ -rw------- 1 root root 15687 Dec 26 13:42 grub.cfg_old lrwxrwxrwx 1 root root 11 Jan 23 2011 home -> home_caiman/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ lrwxrwxrwx 1 root root 23 Dec 29 13:43 home_impala -> /net/impala/home_impala/ lrwxrwxrwx 1 root root 21 Jan 27 08:13 home_lynx2 -> /net/lynx2/home_lynx2/ lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib -> lib64/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log drwx------ 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 4 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 270 root root 0 May 14 14:21 proc/ drwx------ 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ -rw-r--r-- 1 root root 162191459 Jan 13 2011 stage3-amd64-20110113.tar.bz2 dr-xr-xr-x 12 root root 0 May 14 14:21 sys/ drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ Then I did as root: R> source("http://bioconductor.org/biocLite.R") > biocLite("vsn")Save workspace image? [y/n/c]: n root at caiman:/root(15)# ll / total 93 drwxr-xr-x 2 root root 4096 May 16 12:23 bin/ drwxr-xr-x 6 root root 3072 May 14 13:58 boot/ drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/ drwxr-xr-x 21 root root 4040 May 14 14:40 dev/ drwxr-xr-x 160 root root 12288 May 17 17:14 etc/ drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/ drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/ drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/ drwx------ 2 root root 16384 Jan 20 2011 lost+found/ drwxr-xr-x 2 root root 0 May 14 14:21 misc/ drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/ drwxr-xr-x 2 root root 0 May 17 17:38 net/ drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/ dr-xr-xr-x 272 root root 0 May 14 14:21 proc/ drwx------ 36 root root 4096 May 17 15:00 root/ drwxr-xr-x 30 root root 840 May 16 18:21 run/ drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/ dr-xr-xr-x 12 root root 0 May 17 17:38 sys/ drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/ drwxr-xr-x 19 root root 4096 May 6 04:40 usr/ drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/ I.e., all not directory files in / disappeared. This happens on two systems.
Jeff Newmiller
2014-May-18 05:38 UTC
[R] dev-lang/R-3.1.0: biocLite("vsn") removes all files in /
Then you had best not do it again if you don't like that result.
1) This is not the right mailing list for issues having to do with bioconductor.
Please go to the bioconductor mailing list for that.
2) Running random scripts straight from the internet as root without reviewing
them is exactly the kind of thing any experienced *nix user would never do. That
is why user-level accounts have limits on the things they can do. I doubt you
are supposed to be running anything with your current directory set to /, ever,
especially not logged in as root.
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Sent from my phone. Please excuse my brevity.
On May 17, 2014 10:16:46 PM PDT, Juergen Rose <rose at rz.uni-potsdam.de>
wrote:>I had the following files in /:
>
>root at caiman:/root(8)# ll /
>total 160301
>drwxr-xr-x 2 root root 4096 May 16 12:23 bin/
>drwxr-xr-x 6 root root 3072 May 14 13:58 boot/
>-rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log
>lrwxrwxrwx 1 root root 11 Jan 22 2011 data -> data_caiman/
>drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/
>lrwxrwxrwx 1 root root 23 Dec 29 13:43 data_impala ->
>/net/impala/data_impala/
>lrwxrwxrwx 1 root root 21 Jan 27 08:13 data_lynx2 ->
>/net/lynx2/data_lynx2/
>drwxr-xr-x 21 root root 4040 May 14 14:40 dev/
>drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
>-rw------- 1 root root 15687 Dec 26 13:42 grub.cfg_old
>lrwxrwxrwx 1 root root 11 Jan 23 2011 home -> home_caiman/
>drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/
>lrwxrwxrwx 1 root root 23 Dec 29 13:43 home_impala ->
>/net/impala/home_impala/
>lrwxrwxrwx 1 root root 21 Jan 27 08:13 home_lynx2 ->
>/net/lynx2/home_lynx2/
>lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib -> lib64/
>drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/
>drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/
>-rw-r--r-- 1 root root 1797418 May 14 14:22 login.log
>drwx------ 2 root root 16384 Jan 20 2011 lost+found/
>drwxr-xr-x 2 root root 0 May 14 14:21 misc/
>drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/
>drwxr-xr-x 4 root root 0 May 17 17:38 net/
>drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/
>dr-xr-xr-x 270 root root 0 May 14 14:21 proc/
>drwx------ 36 root root 4096 May 17 15:00 root/
>drwxr-xr-x 30 root root 840 May 16 18:21 run/
>drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/
>-rw-r--r-- 1 root root 162191459 Jan 13 2011
>stage3-amd64-20110113.tar.bz2
>dr-xr-xr-x 12 root root 0 May 14 14:21 sys/
>drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/
>drwxr-xr-x 19 root root 4096 May 6 04:40 usr/
>drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/
>
>
>Then I did as root:
>R
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("vsn")
>
>Save workspace image? [y/n/c]: n
>root at caiman:/root(15)# ll /
>total 93
>drwxr-xr-x 2 root root 4096 May 16 12:23 bin/
>drwxr-xr-x 6 root root 3072 May 14 13:58 boot/
>drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/
>drwxr-xr-x 21 root root 4040 May 14 14:40 dev/
>drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
>drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/
>drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/
>drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/
>drwx------ 2 root root 16384 Jan 20 2011 lost+found/
>drwxr-xr-x 2 root root 0 May 14 14:21 misc/
>drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/
>drwxr-xr-x 2 root root 0 May 17 17:38 net/
>drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/
>dr-xr-xr-x 272 root root 0 May 14 14:21 proc/
>drwx------ 36 root root 4096 May 17 15:00 root/
>drwxr-xr-x 30 root root 840 May 16 18:21 run/
>drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/
>dr-xr-xr-x 12 root root 0 May 17 17:38 sys/
>drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/
>drwxr-xr-x 19 root root 4096 May 6 04:40 usr/
>drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/
>
>I.e., all not directory files in / disappeared. This happens on two
>systems.
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
Martin Morgan
2014-May-18 13:30 UTC
[R] dev-lang/R-3.1.0: biocLite("vsn") removes all files in /
This would be very bad and certainly unintended if it were the responsibility of
biocLite. Can we communicate off-list about this? In particular can you report
noquote(readLines("http://bioconductor.org/biocLite.R"))
?
Martin Morgan
On 05/17/2014 10:16 PM, Juergen Rose wrote:> I had the following files in /:
>
> root at caiman:/root(8)# ll /
> total 160301
> drwxr-xr-x 2 root root 4096 May 16 12:23 bin/
> drwxr-xr-x 6 root root 3072 May 14 13:58 boot/
> -rw-r--r-- 1 root root 38673 May 14 14:22 boot_local-d.log
> lrwxrwxrwx 1 root root 11 Jan 22 2011 data -> data_caiman/
> drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/
> lrwxrwxrwx 1 root root 23 Dec 29 13:43 data_impala ->
/net/impala/data_impala/
> lrwxrwxrwx 1 root root 21 Jan 27 08:13 data_lynx2 ->
/net/lynx2/data_lynx2/
> drwxr-xr-x 21 root root 4040 May 14 14:40 dev/
> drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
> -rw------- 1 root root 15687 Dec 26 13:42 grub.cfg_old
> lrwxrwxrwx 1 root root 11 Jan 23 2011 home -> home_caiman/
> drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/
> lrwxrwxrwx 1 root root 23 Dec 29 13:43 home_impala ->
/net/impala/home_impala/
> lrwxrwxrwx 1 root root 21 Jan 27 08:13 home_lynx2 ->
/net/lynx2/home_lynx2/
> lrwxrwxrwx 1 root root 5 Mar 30 04:25 lib -> lib64/
> drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/
> drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/
> -rw-r--r-- 1 root root 1797418 May 14 14:22 login.log
> drwx------ 2 root root 16384 Jan 20 2011 lost+found/
> drwxr-xr-x 2 root root 0 May 14 14:21 misc/
> drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/
> drwxr-xr-x 4 root root 0 May 17 17:38 net/
> drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/
> dr-xr-xr-x 270 root root 0 May 14 14:21 proc/
> drwx------ 36 root root 4096 May 17 15:00 root/
> drwxr-xr-x 30 root root 840 May 16 18:21 run/
> drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/
> -rw-r--r-- 1 root root 162191459 Jan 13 2011
stage3-amd64-20110113.tar.bz2
> dr-xr-xr-x 12 root root 0 May 14 14:21 sys/
> drwxrwxrwt 16 root root 1648 May 17 17:14 tmp/
> drwxr-xr-x 19 root root 4096 May 6 04:40 usr/
> drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/
>
>
> Then I did as root:
> R
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("vsn")
>
> Save workspace image? [y/n/c]: n
> root at caiman:/root(15)# ll /
> total 93
> drwxr-xr-x 2 root root 4096 May 16 12:23 bin/
> drwxr-xr-x 6 root root 3072 May 14 13:58 boot/
> drwxr-xr-x 7 root root 4096 Mar 9 22:29 data_caiman/
> drwxr-xr-x 21 root root 4040 May 14 14:40 dev/
> drwxr-xr-x 160 root root 12288 May 17 17:14 etc/
> drwxr-xr-x 5 root root 4096 Dec 26 11:31 home_caiman/
> drwxr-xr-x 3 root root 4096 May 14 04:31 lib32/
> drwxr-xr-x 17 root root 12288 May 16 12:23 lib64/
> drwx------ 2 root root 16384 Jan 20 2011 lost+found/
> drwxr-xr-x 2 root root 0 May 14 14:21 misc/
> drwxr-xr-x 10 root root 4096 Nov 4 2013 mnt/
> drwxr-xr-x 2 root root 0 May 17 17:38 net/
> drwxr-xr-x 13 root root 4096 Feb 13 13:25 opt/
> dr-xr-xr-x 272 root root 0 May 14 14:21 proc/
> drwx------ 36 root root 4096 May 17 15:00 root/
> drwxr-xr-x 30 root root 840 May 16 18:21 run/
> drwxr-xr-x 2 root root 12288 May 16 12:23 sbin/
> dr-xr-xr-x 12 root root 0 May 17 17:38 sys/
> drwxrwxrwt 19 root root 1752 May 17 18:33 tmp/
> drwxr-xr-x 19 root root 4096 May 6 04:40 usr/
> drwxr-xr-x 16 root root 4096 Dec 26 11:17 var/
>
> I.e., all not directory files in / disappeared. This happens on two
systems.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
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Location: Arnold Building M1 B861
Phone: (206) 667-2793
On Sun, 18 May 2014 07:16:46 +0200 Juergen Rose <rose at rz.uni-potsdam.de> wrote: What disappeared are links and three files. The links are recreatable, although they would be better placed in user space rather than under /. Of the three files, the *bz2 appears to be part of a Gentoo release, the second a grub configuration backup - not needed, and the last a log file. While the locaton of these files and links might be an idiosyncrasy of the Linux distribution you are using, most distributions are inherently more careful in configuration. You should get into the habit of creating a user with more limited scope than root and learn to use "su" and "sudo" if you need super-user rights. Working from root could seriously imperil your system and your work's integrity. JWDougherty